Statistics UMI4C

Creates a stats summary file and generates a summary plot describing statistics for processed UMI-4C samples.

statsUMI4C(wk_dir)

Arguments

wk_dir	Working directory where to save the outputs generated by the UMI-4c analysis.

Value

Returns a plot summarizing the main statistics of the processed UMI-4C experiments found in wk_dir. Also, writes a file named stats_summary.txt in wk_dir/logs that summarizes all the values represented in the plot.

Examples

statsUMI4C(wk_dir = system.file("extdata", "CIITA",
    package = "UMI4Cats"
))
#> Joining, by = "sample_id"
#> Joining, by = "sample_id"
#> Using sample_id as id variables
stats <- read.delim(system.file("extdata", "CIITA", "logs", "stats_summary.txt",
    package = "UMI4Cats"
))
head(stats)
#>         sample_id specific_reads nonspecific_reads filtered_reads filtout_reads
#> 1 ctrl_hi24_CIITA         183831             16169         173342         10489
#> 2 ctrl_hi32_CIITA         183759             16241         181789          1970
#> 3  cyt_hi24_CIITA         181278             18722         178473          2805
#> 4  cyt_hi32_CIITA         183770             16230         182106          1664
#>   al_mapped al_unmapped  umi
#> 1    473730       75809 1115
#> 2    479286       98065 2340
#> 3    479134       90485 1333
#> 4    466677      111822 2198